In May, you can get warm weather, which can be a positive depending on what you prefer. It is still low season, so not as expensive and less tourists. And of course in Tuscany you will see the countryside come to life. In Spring people often feel happier because they are past the cold winter months.
September in my experience is always cool weather, So time for jumpers and light coats. It is slightly less expensive but I found that when I went to Sienna it was still very busy and Venice was unbearable with the crowds.
So, I think my prefernce is Spring.
This year I will be in Tuscany in February, which I expect will be very cold.